This script uses the data.frame “data”, loaded from s01.RData. That is, all rows with C==“C” has been excluded for exploratory data analysis.

# ------------------------------------------------------------------
#  Prepare environment
# ------------------------------------------------------------------
# load packages
source(file=file.path("Scripts","Setup","setup01_projectPackages.R")) 
# load output from s01_DatasetPrep.R
load(file=file.path("Scripts","s01.RData"))

# White background in plots
theme_set(theme_bw()) # to be replaced with a azTheme
update_geom_defaults("point", list(shape = 1))

Are the plots and tables also being written to file?

## [1] TRUE

1 Numeric summaries

The total number of observations in the dataset (with/without BLQ data) and the %BLQ.

## [1] 1491
## [1] 1255
## [1] 15.83

Number of samples and occasions/subject (with/without BLQ)

##       nDV             nOcc      maxTAFD     
##  Min.   :23.00   Min.   :2   Min.   :215.8  
##  1st Qu.:25.00   1st Qu.:2   1st Qu.:215.8  
##  Median :25.00   Median :2   Median :215.8  
##  Mean   :24.85   Mean   :2   Mean   :215.8  
##  3rd Qu.:25.00   3rd Qu.:2   3rd Qu.:215.8  
##  Max.   :25.00   Max.   :2   Max.   :215.8
##       nDV             nOcc      maxTAFD     
##  Min.   :14.00   Min.   :2   Min.   :196.0  
##  1st Qu.:16.00   1st Qu.:2   1st Qu.:198.0  
##  Median :23.00   Median :2   Median :215.8  
##  Mean   :20.92   Mean   :2   Mean   :208.8  
##  3rd Qu.:25.00   3rd Qu.:2   3rd Qu.:215.8  
##  Max.   :25.00   Max.   :2   Max.   :215.8

Number of individuals and samples per dose group

Table 15: Number of individuals and samples per dose group
Dose nSubjects nConc percentBlqByDose
100 15 373 (25) 18.5
150 15 371 (24.9) 8.09
25 15 373 (25) 33.8
300 15 374 (25.1) 2.94


2 Concentrations versus time, stratified by dose and study

2.1 Concentrations vs time after first dose, stratified by study and dose group

Lines connect data from one occasion within a subject. Colour indicate subject. Points indicate measured data. Dashed blue line show the lower limit of quantification. BLQ data is prited as LLOQ/2.

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2.2 Concentrations versus time after dose, stratified by study and dose

Right: un-transformed scale. Left: log-transformed y-axis. Lines connect data from one occasion within a subject. Colour indicate subject. Points indicate measured data. Dashed blue line show the lower limit of quantification. BLQ data is prited as LLOQ/2.

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2.3 Concentrations versus time after dose, stratified by study and dose (zoom)

2.3.1 First 12 hours

Right: un-transformed scale. Left: log-transformed y-axis. Lines connect data from one occasion within a subject. Colour indicate subject. Points indicate measured data. Dashed blue line show the lower limit of quantification. BLQ data is prited as LLOQ/2.

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2.3.2 Absorption phase: first 4 hours

Right: un-transformed scale. Left: log-transformed y-axis. Lines connect data from one occasion within a subject. Colour indicate subject. Points indicate measured data. Dashed blue line show the lower limit of quantification. BLQ data is prited at LLOQ/2.

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2.4 Comparison of single and multiple dose occasions

Right: un-transformed scale. Left: log-transformed y-axis. Lines connect data from one occasion within a subject. Colour indicate subject. Points indicate measured data. Dashed blue line show the lower limit of quantification. BLQ data is prited at LLOQ/2.

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3 Individual plots of concentrations vs time

The section below generates a list of individual plots with different combinations of the following settings:

Not all plots are going to be useful, you can just comment out/delete the ones you do not want to keep.

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